In the autumn of 1861, the Navy asked the firm of Neafie and Levy to construct a small submersible ship designed by the French engineer Brutus DeVilleroi. It wanted such a vessel to counter the threat posed to its wooden-hulled blockaders by the former screw frigate Merrimack which, according to intelligence reports, the Norfolk Navy Yard was rebuilding as an ironclad ram for the Confederacy. Since the Navy's agreement with the Philadelphia shipbuilder specified that the submarine was to be finished in not more than 40 days, her keel was laid down almost immediately following the signing on 1 November 1861 of the contract for her construction. Nevertheless, the work preceeded so slowly that more than four and one-half times 40 days had elapsed when the novel craft finally was launched on 1 May 1862.

Soon after first entering the water, the new boat was towed to the Philadelphia Navy Yard to be fitted out and manned. A fortnight later, a civilian, Mr. Samuel Eakin, was placed in charge of her; and, on 13 June, the Navy formally accepted the small, but unique, ship.

Next, the steam tug Fred Kopp was engaged to tow the submarine to Hampton Roads, Va. The two vessels got underway on 19 June and proceeded down the Delaware River to the Delaware and Chesapeake Canal through which they entered the Chesapeake Bay for the last leg of the voyage. At Norfolk, the submarine was moored alongside the sidewheel steamer, Satellite, her tender during her duty with the North Atlantic Blockading Squadron. A short while after reaching Hampton Roads on the 23d, the submarine picked up the name Alligator, a term which soon appeared in official correspondence.

Several tasks were considered for the strange vessel: destroying a bridge across the Appomattox River; clearing away the obstructions in the James River at Fort Darling which had prevented Union gunboats from steaming upstream to support General McClellan's drive up the peninsula toward Richmond; and blowing up Virginia II if that ironclad were completed and sent downstream to attack Union forces. Consequently, the submarine was sent up the James to City Point where she arrived on the 25th. Comdr. John Rodgers, the senior naval officer in that area, examined Alligator and reported that neither the James off Fort Darling nor the Appomattox near the bridge was deep enough to permit the submarine to submerge completely. Moreover, he feared that, while his theater of operation contained no targets accessible to the submarine, the Union gunboats under his command would be highly vulnerable to her attacks should Alligator fall into enemy hands. As a result, he requested permission to send the submarine back to Hampton Roads.

The ship headed downriver on the 29th and then was ordered to proceed to the Washington Navy Yard for more experimentation and testing. In August, Lt. Thomas O. Selfridge was given command of Alligator; and she was assigned a naval crew. The tests proved to be unsatisfactory, and Selfridge pronounced "the enterprise ... a failure."

The navy yard later removed Alligator's oars and installed a screw propeller in their stead. This change increased her speed to about four knots. On 18 March 1863, President Lincoln observed the submarine in operation.

About this time, Rear Admiral Samual F. Du Pont, who had become interested in the submarine while in command of the Philadelphia Navy Yard early in the war, decided that Alligator might be useful in carrying out his plans to take Charleston, S.C., the birthplace of secession. Acting Master John F. Winchester, who then commanded Sumpter, was ordered to tow the submarine to Port Royal, S.C. The odd pair got underway on 31 March.

The next day, the two ships encountered bad weather which, on 2 April, forced Sumpter to cut Alligator adrift. She soon sank, ending the career of the Navy's first submarine.